Hurricane damage to Puerto Rico’s pharmaceutical industry could hamper the U.S. mainland’s access to critical medications, including treatments for cancer, diabetes and heart disease, the commissioner of the Food and Drug Administration says.

Dr. Scott Gottlieb has said the devastation in Puerto Rico could have broad challenges and implications on the medical product manufacturing base on the island. He called it a “critical health issue for Americans” that could have “significant public health consequences.”

On Friday, Dr. Gottlieb issued a statement saying the FDA is keeping a close watch on the most critical medical products and has stepped in to secure fuel to maintain production lines and logistical support.

Wendy Perry, vice president of the Pharmaceutical Industry Association of Puerto Rico, said Friday that about half of the island’s manufacturing plants were operating, although some only partially.

“Within the next week, we expect the rest of the manufacturing plants to start operating again,” Ms. Perry said by phone from Puerto Rico.

She said her organization is in direct communication with government heads about the priority and importance of bringing the plants back online.

“It’s important to understand we’re managing a situation that, even though we do have the plans, it is a catastrophic hurricane — something we have never seen before. Although we now are in control and we can execute all the plans for the short term, we have to continue to work together with the government in order to address the issues of electricity and telecommunications,” she said.

Puerto Rico’s pharmaceutical manufacturing business is vital to the economy, Ms. Perry said, because it represents 30 percent of the island’s total gross domestic product and provides salaries for employees at almost three times the typical rate for Puerto Ricans.

“That is why we have all the attention and resources from our local government, and I do have to stress the fact that they have been very open, we have communication channels open directly with each one of the heads of the local authorities with whom we have to deal with in order to ensure business continuing,” she said.

Puerto Rico’s drug manufacturing industry employs about 90,000 people and accounts for 72 percent of the island’s exports, representing about $14.5 billion in revenue, according to the U.S. Bureau of Labor Statistics.

Hurricane Maria decimated Puerto Rico when it made landfall on Sept. 20 with sustained winds up to 155 mph, knocking out the power grid of the entire island.

Almost three weeks later, the island is running mostly on generator power, with limited cellphone service and debris blocking transportation routes.

About 50 pharmaceutical companies have manufacturing plants on the island. Although some companies reached for comment said they sustained only minimal or moderate damage, the challenge of operating on generator power is not meant to last more than a few weeks.

Employees are struggling to access their work locations and, along with other Puerto Ricans, are dealing with food, water and fuel shortages.

On the impact on the pharmaceutical supply chain, Dr. Gottlieb has said the FDA is worried about preserving medications, in part by shuttling them off the island, as well as providing relief to Puerto Ricans affected by the storm.

The FDA said it is worried about 40 high-priority drugs but has not named the exact medications that would be in short supply if power is not restored to plants and transportation routes are not cleared.

The FDA said it is working with at least five companies to prevent critical shortages of medical products in Puerto Rico.

Of the companies reached for comment — including Johnson & Johnson, Pfizer, Amgen and Eli Lilly — none reported major damage to its site. The companies said they were using generator power to keep the plants running. They also reported monitoring product inventory levels and supply routes while keeping manufacturing levels up at other international sites.

Among the products produced on the island are life-saving medications used to treat cancer, diabetes, cardiovascular diseases and HIV.

“Overall, our facilities fared very well given the magnitude of the storm, and we’ve begun to restart some operations under generator power,” Johnson & Johnson spokesman Ernie Knewitz said in an email. The company has about 3,600 employees and operates seven facilities on the island.

“We have a strong local team working through incredible logistical challenges, and we’re seeing progress each day. We are also closely monitoring our product inventory levels and will work to ensure all critical needs are met,” Mr. Knewitz said.

Pfizer said in a statement that it is working to repair damage and restore electricity to its facilities, relying on generator power and unsure how long it will be until power is restored.

“Overall, we have a healthy supply of finished goods available for patients and do not currently see a risk to patient supply,” the company said. “We are monitoring the supply situation closely and utilizing alternative manufacturing locations where possible. We remain in regular contact with the FDA and regulators from other countries.”

A spokesman for Eli Lilly, known for making diabetes medication as well as cancer and cardiovascular drugs, said its facilities were built to withstand hurricane conditions and that preparations before the storms included halting production, locking down facilities and instructing employees to stay home.

“Our inventory strategy for products is designed to protect against this type of event, and we see no product supply risk to global markets at this time. The affiliate sustained minimal damage as well,” the company said in a statement.

Nicolette Louissaint is executive director of Healthcare Ready, which helps coordinate with public and private entities to ensure a supply chain of medical equipment to disaster areas. She said Hurricane Maria’s devastating effects on the island and logistical challenges have slowed relief efforts.

“We still are learning about the overall impacts, especially the health impacts of Maria,” Ms. Louissaint said. “One of the things that we have to continue to think about is how we track and care for the patients that are still at risk. There have been reports that are coming out, and we’re starting to learn more about what the true medical needs are, but keeping our eye on that is going to be really important over the next few weeks, especially.”

Healthcare Ready has been working for six weeks straight to respond to the needs of people caught in the paths of Hurricanes Harvey, Irma and Maria.

Ms. Louissaint said Puerto Rico is still about 94 percent without power with only 12 percent cell reception. While hospitals, and some people, are powering with generators, damage to roads has slowed access to diesel and gasoline.

“We’re starting to see that gasoline is becoming more available, and that really is important because it allows people to start to go to work,” she said.